Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Atrx

Cell type

Cell type Class
Neural
Cell type
Neuroepithelial progenitor cell
NA
NA

Attributes by original data submitter

Sample

source_name
Tp53+/+ NPC
tissue
forebrain
cell type
Neuroepithelial progenitor cell
passage
8-10
strain
mixed
genotype
Tp53+/+
chip antibody
ATRX H300 antibody (Santa Cruz)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and ATRX-DNA complexes were isolated with antibody. ATRX ChIP was performed as previously described (Law et al., 2010). Cells were fixed with 2 mM EGS (Pierce) for 45 min at room temperature in PBS. Formaldehyde was then added to 1% for 20 min and quenched with 125 mM glycine. Chromatin was sonicated with a Bioruptor Plus (Diagenode) to generate DNA fragments under 500 bp and lysates were immunoprecipitated with 40 μg ATRX H300 antibody or rabbit IgG control (Santa Cruz Biotechnology).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
44898255
Reads aligned (%)
93.3
Duplicates removed (%)
27.2
Number of peaks
22188 (qval < 1E-05)

mm9

Number of total reads
44898255
Reads aligned (%)
93.0
Duplicates removed (%)
27.1
Number of peaks
23062 (qval < 1E-05)

Base call quality data from DBCLS SRA